* allow to change the compression level in BAM output

[samtools.git] / bcftools / vcfutils.pl

diff --git a/bcftools/vcfutils.pl b/bcftools/vcfutils.pl
index 12807c6d40d0af9b05fbdfd8d3065b68623ac0be..6ced66a2893e9b98884774e88607e9f2060af3d1 100755 (executable)
--- a/bcftools/vcfutils.pl
+++ b/bcftools/vcfutils.pl
@@ -201,7 +201,7 @@ Note: This command discards indels. Output: QUAL #non-indel #SNPs #transitions #
          my @x;
          $x[0] = sprintf("%.4f", $c[1]-$c[2]? $c[2] / ($c[1] - $c[2]) : 100);
          $x[1] = sprintf("%.4f", $hsize? $c[3] / $hsize : 0);
-         $x[2] = sprintf("%.4f", $c[1] ? $c[3] / $c[1] : 0);
+         $x[2] = sprintf("%.4f", $c[3] / $c[1]);
          my $a = $c[1] - $lc[1];
          my $b = $c[2] - $lc[2];
          $x[3] = sprintf("%.4f", $a-$b? $b / ($a-$b) : 100);
@@ -512,7 +512,7 @@ Options: -d INT    minimum depth          [$opts{d}]
          $q = chr($q <= 126? $q : 126);
          $seq .= $b;
          $qual .= $q;
-       } else { # an INDEL
+       } elsif ($t[4] ne '.') { # an INDEL
          push(@gaps, [$t[1], length($t[3])]);
        }
        $last_pos = $t[1];